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2,164 results on '"Zhang, Ya-Ping"'

1. Negative refraction with little loss manipulated by the voltage and pulsed laser in double quantum dots

Author

Zhao, Shun-Cai, Qian, Xiao-fan, Zhang, Ya-Ping, and Zhang, Yong-An

Subjects
Physics - Optics, Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

The paper demonstrates that negative refractive index can be achieved via tuning the tunneling rate between a double quantum dots(QDs) system by applying a bias voltage, and a pulsed laser. As the bias voltage being changed, the refraction index can be tunable to negative with the simultaneous negative permittivity and permeability. While the varying pulsed laser is applied to the double QDs system, moreover, the negative refractive index with little loss can be obtained. The flexible manipulation on a solid state system to realize negative refraction may give a new way for experimental research in the future., Comment: 10 pages, 6 figures

Published
2024
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5. Author Correction: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer R. S., Kidd, Jefrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew J., Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, André, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytönen, Marjo K., Kalthof, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Published
2023
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6. Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau

Author

Peng, Min-Sheng, Liu, Yan-Hu, Shen, Quan-Kuan, Zhang, Xiao-Hua, Dong, Jiajia, Li, Jin-Xiu, Zhao, Hui, Zhang, Hui, Zhang, Xiaoming, He, Yaoxi, Shi, Hong, Cui, Chaoying, Ouzhuluobu, Wu, Tian-Yi, Liu, Shi-Ming, Gonggalanzi, Baimakangzhuo, Bai, Caijuan, Duojizhuoma, Liu, Ti, Dai, Shan-Shan, Murphy, Robert W., Qi, Xue-Bin, Dong, Guanghui, Su, Bing, and Zhang, Ya-Ping

Published
2023
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7. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

Author

Meadows, Jennifer R. S., Kidd, Jeffrey M., Wang, Guo-Dong, Parker, Heidi G., Schall, Peter Z., Bianchi, Matteo, Christmas, Matthew J., Bougiouri, Katia, Buckley, Reuben M., Hitte, Christophe, Nguyen, Anthony K., Wang, Chao, Jagannathan, Vidhya, Niskanen, Julia E., Frantz, Laurent A. F., Arumilli, Meharji, Hundi, Sruthi, Lindblad-Toh, Kerstin, Ginja, Catarina, Agustina, Kadek Karang, André, Catherine, Boyko, Adam R., Davis, Brian W., Drögemüller, Michaela, Feng, Xin-Yao, Gkagkavouzis, Konstantinos, Iliopoulos, Giorgos, Harris, Alexander C., Hytönen, Marjo K., Kalthoff, Daniela C., Liu, Yan-Hu, Lymberakis, Petros, Poulakakis, Nikolaos, Pires, Ana Elisabete, Racimo, Fernando, Ramos-Almodovar, Fabian, Savolainen, Peter, Venetsani, Semina, Tammen, Imke, Triantafyllidis, Alexandros, vonHoldt, Bridgett, Wayne, Robert K., Larson, Greger, Nicholas, Frank W., Lohi, Hannes, Leeb, Tosso, Zhang, Ya-Ping, and Ostrander, Elaine A.

Published
2023
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10. Large-scale genomic analysis reveals the genetic cost of chicken domestication

Author

Wang, Ming-Shan, Zhang, Jin-Jin, Guo, Xing, Li, Ming, Meyer, Rachel, Ashari, Hidayat, Zheng, Zhu-Qing, Wang, Sheng, Peng, Min-Sheng, Jiang, Yu, Thakur, Mukesh, Suwannapoom, Chatmongkon, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Kharrati-Koopaee, Hamed, Zeng, Lin, Wang, Yun-Mei, Yin, Ting-Ting, Yang, Min-Min, Li, Ming-Li, Lu, Xue-Mei, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasig, Thilina Madusanka, Feng, Shao-Hong, Zhang, Hao, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Thuy, Le Thi, Mwai, Okeyo A, Ibrahim, Mohamed Nawaz Mohamed, Zhang, Guojie, Qu, Kai-Xing, Hanotte, Olivier, Shapiro, Beth, Bosse, Mirte, Wu, Dong-Dong, Han, Jian-Lin, and Zhang, Ya-Ping

Subjects
Biotechnology, Genetics, Human Genome, Animals, Animals, Domestic, Chickens, Domestication, Genome, Genomics, Humans, Bottleneck, Genetic load, Deleterious mutation, Domestic chicken, Developmental Biology
Abstract

BackgroundSpecies domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.ResultsWe analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.ConclusionThis study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Published
2021

14. Individual-Level SNP Diversity and Similarity Profiles

Author

Zhanshan, Ma, Li, Lianwei, and Zhang, Ya-Ping

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Classic concepts of genetic (gene) diversity (heterozygosity) such as Nei (1973: PNAS) and Nei and Li (1979: PNAS) nucleotide diversity were defined within the context of populations. Although variations are often measured in population context, the basic carriers of variation are individuals. Hence, measuring variations such as SNP of individual against a reference genome, which has been ignored currently, is certainly of its own right. Indeed, similar practice has been a tradition in ecology, where the basic framework of diversity measure is individual community sample. We propose to use Renyi-entropy-derived Hill numbers to define SNP (single nucleotide polymorphism) diversity (including alpha-, beta-, and gamma-diversities) and similarity profiles. Hill numbers are derived from Renyi entropy, of which Shannon entropy is a special case and which have found widely applications including measuring the quantum information entanglement, wealth distribution in economics and ecological diversity. The newly proposed SNP diversity not only complements the existing genetic diversity concepts by offering individual-level metrics, but also offers building blocks for comparative genetic analysis at higher levels. The profile concept also helps to resolve a dilemma in measuring diversity: the choice from various diversity indexes, because diversity profile unifies some of the most commonly used indexes (as special cases) with different diversity orders (along the rareness-commonness spectrum of gene mutations). Finally, the profiles can be estimated with rarefaction approach, which may help to relieve some effect of insufficient sequencing coverage.

Published
2019

15. Author Correction: 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Biochemistry and Cell Biology, Biological Sciences, Clinical Sciences, Developmental Biology, Biochemistry and cell biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

16. Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids

Author

Wang, Ming-Shan, Wang, Sheng, Li, Yan, Jhala, Yadvendradev, Thakur, Mukesh, Otecko, Newton O, Si, Jing-Fang, Chen, Hong-Man, Shapiro, Beth, Nielsen, Rasmus, Zhang, Ya-Ping, and Wu, Dong-Dong

Subjects
Human Genome, Genetics, Generic health relevance, Animals, Basic Helix-Loop-Helix Transcription Factors, Biological Evolution, Dogs, Hybridization, Genetic, Whole Genome Sequencing, Wolves, genetic introgression, phylogeny, EPAS1, high-altitude adaptation, dog and wolf, EPAS1, hybridization, adaptive evolution, evolutionary history, canid, introgression, Biochemistry and Cell Biology, Evolutionary Biology
Abstract

Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

Published
2020

17. 863 genomes reveal the origin and domestication of chicken

Author

Wang, Ming-Shan, Thakur, Mukesh, Peng, Min-Sheng, Jiang, Yu, Frantz, Laurent Alain François, Li, Ming, Zhang, Jin-Jin, Wang, Sheng, Peters, Joris, Otecko, Newton Otieno, Suwannapoom, Chatmongkon, Guo, Xing, Zheng, Zhu-Qing, Esmailizadeh, Ali, Hirimuthugoda, Nalini Yasoda, Ashari, Hidayat, Suladari, Sri, Zein, Moch Syamsul Arifin, Kusza, Szilvia, Sohrabi, Saeed, Kharrati-Koopaee, Hamed, Shen, Quan-Kuan, Zeng, Lin, Yang, Min-Min, Wu, Ya-Jiang, Yang, Xing-Yan, Lu, Xue-Mei, Jia, Xin-Zheng, Nie, Qing-Hua, Lamont, Susan Joy, Lasagna, Emiliano, Ceccobelli, Simone, Gunwardana, Humpita Gamaralalage Thilini Nisanka, Senasige, Thilina Madusanka, Feng, Shao-Hong, Si, Jing-Fang, Zhang, Hao, Jin, Jie-Qiong, Li, Ming-Li, Liu, Yan-Hu, Chen, Hong-Man, Ma, Cheng, Dai, Shan-Shan, Bhuiyan, Abul Kashem Fazlul Haque, Khan, Muhammad Sajjad, Silva, Gamamada Liyanage Lalanie Pradeepa, Le, Thi-Thuy, Mwai, Okeyo Ally, Ibrahim, Mohamed Nawaz Mohamed, Supple, Megan, Shapiro, Beth, Hanotte, Olivier, Zhang, Guojie, Larson, Greger, Han, Jian-Lin, Wu, Dong-Dong, and Zhang, Ya-Ping

Subjects
Genetics, Animal Distribution, Animals, Animals, Domestic, Asia, Chickens, Domestication, Gene Pool, Genome, Geography, Likelihood Functions, Phylogeny, Poultry, Selection, Genetic, Biochemistry and Cell Biology, Clinical Sciences, Developmental Biology
Abstract

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Published
2020

18. Heterologous Expression of Dehydration-Inducible MfWRKY17 of Myrothamnus Flabellifolia Confers Drought and Salt Tolerance in Arabidopsis

Author

Huang, Zhuo, Guo, Han-Du, Liu, Ling, Jin, Si-Han, Zhu, Pei-Lei, Zhang, Ya-Ping, and Jiang, Cai-Zhong

Subjects
Plant Biology, Biological Sciences, Genetics, Adaptation, Physiological, Arabidopsis, Arabidopsis Proteins, Dehydration, Droughts, Gene Expression Regulation, Plant, Magnoliopsida, Plant Proteins, Plants, Genetically Modified, Salt Tolerance, Stress, Physiological, Transcription Factors, Myrothamnus flabellifolia, resurrection plant, drought tolerance, gene function, molecular mechanism, WRKY transcription factor, Other Chemical Sciences, Other Biological Sciences, Chemical Physics, Biochemistry and cell biology, Microbiology, Medicinal and biomolecular chemistry
Abstract

: As the only woody resurrection plant, Myrothamnus flabellifolia has a strong tolerance to drought and can survive long-term in a desiccated environment. However, the molecular mechanisms related to the stress tolerance of M. flabellifolia are largely unknown, and few tolerance-related genes previously identified had been functionally characterized. WRKYs are a group of unique and complex plant transcription factors, and have reported functions in diverse biological processes, especially in the regulation of abiotic stress tolerances, in various species. However, little is known about their roles in response to abiotic stresses in M. flabellifolia. In this study, we characterized a dehydration-inducible WRKY transcription factor gene, MfWRKY17, from M. flabellifolia. MfWRKY17 shows high degree of homology with genes from Vitis vinifera and Vitis pseudoreticulata, belonging to group II of the WRKY family. Unlike known WRKY17s in other organisms acting as negative regulators in biotic or abiotic stress responses, overexpression of MfWRKY17 in Arabidopsis significantly increased drought and salt tolerance. Further investigations indicated that MfWRKY17 participated in increasing water retention, maintaining chlorophyll content, and regulating ABA biosynthesis and stress-related gene expression. These results suggest that MfWRKY17 possibly acts as a positive regulator of stress tolerance in the resurrection plant M. flabellifolia.

Published
2020

19. The Method of Division and Classification Quantification for Snow and Ice Removal on Airport Pavement

Author

Zhang, Ya-ping, Zhang, Yu, Xing, Xiao-qing, Chen, Ye, Yang, Nan, Mao, Jian, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Wang, Wuhong, editor, Chen, Yanyan, editor, He, Zhengbing, editor, and Jiang, Xiaobei, editor

Published
2022
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20. Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish

Author

Wang, Yang, Li, Xi-Yin, Xu, Wen-Jie, Wang, Kun, Wu, Bin, Xu, Meng, Chen, Yan, Miao, Li-Jun, Wang, Zhong-Wei, Li, Zhi, Zhang, Xiao-Juan, Yin, Zhan, Zhou, Bo-Tong, Yang, Yu-Lan, Zhu, Cheng-Long, Hu, Ming-Liang, Zheng, Jiang-Ming, Feng, Chen-Guang, Qiu, Qiang, Tian, Le-Tian, Lu, Meng, Peng, Fang, Lu, Wei-Jia, Tong, Jin-Feng, Tong, Jin-Gou, Fu, Bei-De, Yu, Peng, Ding, Miao, Gan, Rui-Hai, Zhang, Qin-Qin, Jian, Jian-Bo, Zhang, Chi, He, Wei-Ming, Yang, Wei, Zhao, Zi-Cheng, Zhang, Qian-Qian, Gao, Qiang, Xu, Jun-Yang, Bai, Ming-Zhou, Zhang, Ya-Ping, Yang, Huan-Ming, Fang, Xiao-Dong, Wang, Wen, Zhou, Li, and Gui, Jian-Fang

Published
2022
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21. Rapid evolution of fine-scale recombination during domestication

Author

Liu, Zheng-Xi, primary, Li, Ming, additional, Si, Si, additional, Chen, Jian-Hai, additional, Hu, Li-Rong, additional, Peng, Min-Sheng, additional, Yin, Ting-Ting, additional, Esmailizadeh, Ali, additional, Zhang, Chang, additional, Qu, Lu-Jiang, additional, Lu, Xue-Mei, additional, Han, Jian-Lin, additional, Zhang, Ya-Ping, additional, and Wang, Ming-Shan, additional

Published
2024
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22. Hidden hotspots of amphibian biodiversity in China

Author

Xu, Wei, primary, Wu, Yun-He, additional, Zhou, Wei-Wei, additional, Chen, Hong-Man, additional, Zhang, Bao-Lin, additional, Chen, Jin-Min, additional, Xu, Weihua, additional, Rao, Ding-Qi, additional, Zhao, Haipeng, additional, Yan, Fang, additional, Yuan, Zhiyong, additional, Jiang, Ke, additional, Jin, Jie-Qiong, additional, Hou, Mian, additional, Zou, Dahu, additional, Wang, Li-Jun, additional, Zheng, Yuchi, additional, Li, Jia-Tang, additional, Jiang, Jianping, additional, Zeng, Xiao-Mao, additional, Chen, Youhua, additional, Liao, Zi-Yan, additional, Li, Cheng, additional, Li, Xue-You, additional, Gao, Wei, additional, Wang, Kai, additional, Zhang, Dong-Ru, additional, Lu, Chenqi, additional, Yin, Tingting, additional, Ding, Zhaoli, additional, Zhao, Gui-Gang, additional, Chai, Jing, additional, Zhao, Wen-Ge, additional, Zhang, Ya-Ping, additional, Wiens, John J., additional, and Che, Jing, additional

Published
2024
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25. Crystal structure of [diaqua-bis(2-((1H-tetrazol-1-yl)methyl)-5-carboxy-1H-imidazole-4-carboxylato-κ2 N,O) manganese(II)] dihydrate, C14H18MnN12O12

Author

Zhang Ya-Ping and Li Zu-Tian

Subjects
2190558, Physics, QC1-999, Crystallography, QD901-999
Abstract

C14H18MnN12O12, monoclinic, P21/c (no. 14), a = 9.333(7) Å, b = 19.038(13) Å, c = 7.042(5) Å, β = 111.989(10)°, V = 1160.2(14) Å3, Z = 2, Rgt (F) = 0.0301, wRref (F 2) = 0.0809, T = 293(2) K.

Published
2022
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28. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics

Author

Mauki, David H., Tijjani, Abdulfatai, Ma, Cheng, Ng’ang’a, Said I., Mark, Akanbi I., Sanke, Oscar J., Abdussamad, Abdussamad M., Olaogun, Sunday C., Ibrahim, Jebi, Dawuda, Philip M., Mangbon, Godwin F., Kazwala, Rudovick R., Gwakisa, Paul S., Yin, Ting-Ting, Li, Yan, Peng, Min-Sheng, Adeola, Adeniyi C., and Zhang, Ya-Ping

Published
2022
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31. Puzzle Hi-C: An accurate scaffolding software.

Author

Lin, Guoliang, Huang, Zhiru, Yue, Tingsong, Chai, Jing, Li, Yan, Yang, Huimin, Qin, Wanting, Yang, Guobing, Murphy, Robert W., Zhang, Ya-ping, Zhang, Zijie, Zhou, Wei, and Luo, Jing

Subjects
COMPARATIVE genomics, GENOMICS, PUZZLES, CHROMOSOMES, COMPUTER software
Abstract

High-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data. Curation of genomes reveal that current Hi-C-assisted scaffolding algorithms either generate ordering and orientation errors or fail to assemble high-quality chromosome-level scaffolds. Here, we offer the software Puzzle Hi-C, which uses Hi-C reads to accurately assign contigs or scaffolds to chromosomes. Puzzle Hi-C uses the triangle region instead of the square region to count interactions in a Hi-C heatmap. This strategy dramatically diminishes scaffolding interference caused by long-range interactions. This software also introduces a dynamic, triangle window strategy during assembly. Initially small, the window expands with interactions to produce more effective clustering. Puzzle Hi-C outperforms available scaffolding tools. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Pervasive introgression facilitated domestication and adaptation in the Bos species complex

Author

Wu, Dong-Dong, Ding, Xiang-Dong, Wang, Sheng, Wójcik, Jan M, Zhang, Yi, Tokarska, Małgorzata, Li, Yan, Wang, Ming-Shan, Faruque, Omar, Nielsen, Rasmus, Zhang, Qin, and Zhang, Ya-Ping

Subjects
Biotechnology, Genetics, Human Genome, Generic health relevance, Adaptation, Biological, Animals, Biological Evolution, Bison, Cattle, Domestication, Genetic Variation, Genome, Hybridization, Genetic
Abstract

Species of the Bos genus, including taurine cattle, zebu, gayal, gaur, banteng, yak, wisent and bison, have been domesticated at least four times and have been an important source of meat, milk and power for many human cultures. We sequence the genomes of gayal, gaur, banteng, wisent and bison, and provide population genomic sequencing of an additional 98 individuals. We use these data to determine the phylogeny and evolutionary history of these species and show that the threatened gayal is an independent species or subspecies. We show that there has been pronounced introgression among different members of this genus, and that it in many cases has involved genes of considerable adaptive importance. For example, genes under domestication selection in cattle (for example, MITF) were introgressed from domestic cattle to yak. Also, genes in the response-to-hypoxia pathway (for example, EGLN1, EGLN2 and HIF3a) have been introgressed from yak to Tibetan cattle, probably facilitating their adaptation to high altitude. We also validate that there is an association between the introgressed EGLN1 allele and haemoglobin and red blood cell concentration. Our results illustrate the importance of introgression as a source of adaptive variation and during domestication, and suggest that the Bos genus evolves as a complex of genetically interconnected species with shared evolutionary trajectories.

Published
2018

33. Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri

Author

Wang, Guo-Dong, Zhang, Bao-Lin, Zhou, Wei-Wei, Li, Yong-Xin, Jin, Jie-Qiong, Shao, Yong, Yang, He-Chuan, Liu, Yan-Hu, Yan, Fang, Chen, Hong-Man, Jin, Li, Gao, Feng, Zhang, Yaoguang, Li, Haipeng, Mao, Bingyu, Murphy, Robert W, Wake, David B, Zhang, Ya-Ping, and Che, Jing

Subjects
Human Genome, Genetics, Animals, Anura, Gene Flow, Genetic Speciation, Hybridization, Genetic, Metagenomics, Phylogeny, Selection, Genetic, Tibet, gene flow, hybridization, natural selection, population genomics, speciation
Abstract

Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.

Published
2018

34. Puzzle Hi-C: an accurate scaffolding software

Author

Lin, Guoliang, primary, Huang, Zhiru, additional, Yue, Tingsong, additional, Chai, Jing, additional, Li, Yan, additional, Yang, Huimin, additional, Qin, Wanting, additional, Yang, Guobing, additional, Murphy, Robert W., additional, Zhang, Ya-ping, additional, Zhang, Zijie, additional, Zhou, Wei, additional, and Luo, Jing, additional

Published
2024
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35. On the origin of SARS-CoV-2—The blind watchmaker argument

Author

Wu, Chung-I, Wen, Haijun, Lu, Jian, Su, Xiao-dong, Hughes, Alice C., Zhai, Weiwei, Chen, Chen, Chen, Hua, Li, Mingkun, Song, Shuhui, Qian, Zhaohui, Wang, Qihui, Chen, Bingjie, Guo, Zixiao, Ruan, Yongsen, Lu, Xuemei, Wei, Fuwen, Jin, Li, Kang, Le, Xue, Yongbiao, Zhao, Guoping, and Zhang, Ya-Ping

Published
2021
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40. Analysis of Influencing Factors of Integrated Freight Transport Volume Based on Gray Markov Model

Author

Zhang, Ya-ping, Gao, Yue-e, Xie, Yan-wen, Qi, Shou-ming, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Ruediger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Liang, Qilian, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zhang, Junjie James, Series Editor, Wang, Wuhong, editor, Bengler, Klaus, editor, and Jiang, Xiaobei, editor

Published
2019
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41. Research of Model on Connectivity of Road Network Considering Traffic Flow Status in China

Author

Zhang, Ya-ping, Qi, Tao, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Ruediger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Liang, Qilian, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zhang, Junjie James, Series Editor, Wang, Wuhong, editor, Bengler, Klaus, editor, and Jiang, Xiaobei, editor

Published
2019
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43. Mitochondrial Genomes of Domestic Animals Need Scrutiny

Author

Shi, Ni-Ni, Fan, Long, Yao, Yong-Gang, Peng, Min-Sheng, and Zhang, Ya-Ping

Subjects
Quantitative Biology - Populations and Evolution
Abstract

More than 1000 complete or near-complete mitochondrial DNA (mtDNA) sequences have been deposited in GenBank for eight common domestic animals (i.e. cattle, dog, goat, horse, pig, sheep, yak and chicken) and their close wild ancestors or relatives. Nevertheless, few efforts have been performed to evaluate the sequence data quality, which heavily impact the original conclusion. Herein, we conducted a phylogenetic survey of these complete or near-complete mtDNA sequences based on mtDNA haplogroup trees for the eight animals. We show that, errors due to artificial recombination, surplus of mutations, and phantom mutations, do exist in 14.5% (194/1342) of mtDNA sequences and shall be treated with wide caution. We propose some caveats for mtDNA studies of domestic animals in the future., Comment: 129 Pages, 1 figure, 3 tables, and 5 supplementary materials

Published
2014

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